-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
- * AM Waterhouse
- *******************/
-
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
package jalview.jbgui;
-import javax.swing.*;
-import java.awt.event.*;
import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
-public class GAlignFrame extends JInternalFrame
+import jalview.schemes.*;
+import java.awt.BorderLayout;
+
+public class GAlignFrame
+ extends JInternalFrame
{
protected JMenuBar alignFrameMenuBar = new JMenuBar();
protected JMenu fileMenu = new JMenu();
protected JMenu viewMenu = new JMenu();
protected JMenu colourMenu = new JMenu();
protected JMenu calculateMenu = new JMenu();
- protected JMenu alignMenu = new JMenu();
- protected JMenuItem groupsMenuItem = new JMenuItem();
+ protected JMenu webService = new JMenu();
+ protected JMenuItem webServiceNoServices;
protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
protected JMenuItem invertSequenceMenuItem = new JMenuItem();
- protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
protected JMenuItem remove2LeftMenuItem = new JMenuItem();
protected JMenuItem remove2RightMenuItem = new JMenuItem();
protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
- protected JMenuItem setGapCharMenuItem = new JMenuItem();
- protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
protected JMenuItem sortIDMenuItem = new JMenuItem();
protected JMenuItem sortGroupMenuItem = new JMenuItem();
- protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
protected JMenuItem PCAMenuItem = new JMenuItem();
protected JMenuItem clustalAlignMenuItem = new JMenuItem();
BorderLayout borderLayout1 = new BorderLayout();
public JLabel statusBar = new JLabel();
- protected JMenu saveAlignmentMenu = new JMenu();
+ protected JMenuItem saveAlignmentMenu = new JMenuItem();
protected JMenu outputTextboxMenu = new JMenu();
protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem hydrophobicityColour = new
+ JRadioButtonMenuItem();
protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
JMenuItem njTreeBlosumMenuItem = new JMenuItem();
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
- protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
JMenuItem htmlMenuItem = new JMenuItem();
JMenuItem overviewMenuItem = new JMenuItem();
protected JMenuItem undoMenuItem = new JMenuItem();
protected JMenuItem redoMenuItem = new JMenuItem();
- protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
- protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
JMenuItem printMenuItem = new JMenuItem();
- protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
JMenuItem findMenuItem = new JMenuItem();
JMenu searchMenu = new JMenu();
- protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
JMenuItem deleteGroups = new JMenuItem();
JMenuItem delete = new JMenuItem();
JMenu jMenu1 = new JMenu();
JMenuItem pasteNew = new JMenuItem();
JMenuItem pasteThis = new JMenuItem();
- protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
JMenuItem createPNG = new JMenuItem();
protected JMenuItem font = new JMenuItem();
- protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
JMenuItem epsFile = new JMenuItem();
JMenuItem LoadtreeMenuItem = new JMenuItem();
- JMenuItem jpred = new JMenuItem();
+ public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+ public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+ protected JMenuItem modifyPID = new JMenuItem();
+ protected JMenuItem modifyConservation = new JMenuItem();
+ protected JMenu sortByTreeMenu = new JMenu();
+ protected JMenu sort = new JMenu();
+ JMenu calculate = new JMenu();
+ JMenu jMenu2 = new JMenu();
+ protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
+ protected ButtonGroup colours = new ButtonGroup();
+ JMenuItem vamsasStore = new JMenuItem();
+ protected JMenuItem showTranslation = new JMenuItem();
+ public JMenuItem featureSettings = new JMenuItem();
+ JMenuItem fetchSequence = new JMenuItem();
+ protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();
+ JMenuItem annotationColour = new JMenuItem();
+ JMenuItem associatedData = new JMenuItem();
+ protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
+ JMenu addSequenceMenu = new JMenu();
+ JMenuItem addFromFile = new JMenuItem();
+ JMenuItem addFromText = new JMenuItem();
+ JMenuItem addFromURL = new JMenuItem();
+ JMenuItem exportAnnotations = new JMenuItem();
+ JMenuItem exportFeatures = new JMenuItem();
+ protected JPanel statusPanel = new JPanel();
+ GridLayout gridLayout1 = new GridLayout();
+ JMenu jMenu3 = new JMenu();
+ JMenuItem showAllSeqs = new JMenuItem();
+ JMenuItem showAllColumns = new JMenuItem();
+ JMenu jMenu4 = new JMenu();
+ JMenuItem hideSelSequences = new JMenuItem();
+ JMenuItem hideSelColumns = new JMenuItem();
+ protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
+ JMenuItem invertColSel = new JMenuItem();
+
public GAlignFrame()
{
jbInit();
setJMenuBar(alignFrameMenuBar);
- JMenuItem item;
// dynamically fill save as menu with available formats
- for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
- item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
- saveAlignmentMenu.add( item );
- item.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- saveAs_actionPerformed(e);
- }
- });
+ for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+ {
+ JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
- item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
- outputTextboxMenu.add( item );
+ outputTextboxMenu.add(item);
}
-
}
- catch(Exception e)
+ catch (Exception e)
{
- e.printStackTrace();
}
- ButtonGroup colours = new ButtonGroup();
+
+ if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
+ {
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+ getUserColourSchemes().keys();
+
+ while (userColours.hasMoreElements())
+ {
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+ nextElement().toString());
+ radioItem.setName("USER_DEFINED");
+ radioItem.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent evt)
+ {
+ if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+ {
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+ int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
+ "Remove from default list?",
+ "Remove user defined colour",
+ JOptionPane.YES_NO_OPTION);
+ if(option == JOptionPane.YES_OPTION)
+ {
+ jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
+ colourMenu.remove(radioItem);
+ }
+ else
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+ }
+ }
+ });
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+ colourMenu.insert(radioItem, 15);
+ colours.add(radioItem);
+ }
+ }
colours.add(noColourmenuItem);
colours.add(clustalColour);
colours.add(zappoColour);
colours.add(PIDColour);
colours.add(BLOSUM62Colour);
colours.add(nucleotideColour);
+
+ setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
+
+
+ }
+
+ public void setColourSelected(String defaultColour)
+ {
+
+ if (defaultColour != null)
+ {
+ int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
+
+ switch (index)
+ {
+ case ColourSchemeProperty.NONE:
+ noColourmenuItem.setSelected(true);
+ break;
+ case ColourSchemeProperty.CLUSTAL:
+ clustalColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.BLOSUM:
+ BLOSUM62Colour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.PID:
+ PIDColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.ZAPPO:
+ zappoColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.TAYLOR:
+ taylorColour.setSelected(true);
+ break;
+
+ case ColourSchemeProperty.HYDROPHOBIC:
+ hydrophobicityColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.HELIX:
+ helixColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.STRAND:
+ strandColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.TURN:
+ turnColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.BURIED:
+ buriedColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.NUCLEOTIDE:
+ nucleotideColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.USER_DEFINED:
+ userDefinedColour.setSelected(true);
+
+ break;
+ }
+ }
+
}
- private void jbInit() throws Exception
+
+ private void jbInit()
+ throws Exception
{
fileMenu.setMnemonic('F');
fileMenu.setText("File");
saveAlignmentMenu.setMnemonic('L');
- saveAlignmentMenu.setText("Save alignment to local file");
+ saveAlignmentMenu.setText("Save As");
+ saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
+ awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));
+ saveAlignmentMenu.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ saveAlignmentMenu_actionPerformed(e);
+ }
+ });
closeMenuItem.setMnemonic('C');
closeMenuItem.setText("Close");
closeMenuItem.addActionListener(new java.awt.event.ActionListener()
viewMenu.setText("View");
colourMenu.setText("Colour");
calculateMenu.setText("Calculate");
- alignMenu.setText("Web Service");
- groupsMenuItem.setVisible(false);
- groupsMenuItem.setText("Groups");
- groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- groupsMenuItem_actionPerformed(e);
- }
- });
+ webService.setText("Web Service");
selectAllSequenceMenuItem.setText("Select all");
- selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+ selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_A,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ selectAllSequenceMenuItem.addActionListener(new java.awt.event.
+ ActionListener()
{
public void actionPerformed(ActionEvent e)
{
selectAllSequenceMenuItem_actionPerformed(e);
}
});
- deselectAllSequenceMenuItem.setText("Clear selection");
- deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+ deselectAllSequenceMenuItem.setText("Deselect All");
+ deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
+ getKeyStroke(
+ java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
+ deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
+ ActionListener()
{
public void actionPerformed(ActionEvent e)
{
deselectAllSequenceMenuItem_actionPerformed(e);
}
});
- invertSequenceMenuItem.setText("Invert sequence selection");
+ invertSequenceMenuItem.setText("Invert Sequence Selection");
invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
invertSequenceMenuItem_actionPerformed(e);
}
});
- deselectAllColumnsMenuItem.setText("Deselect all columns");
- deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- deselectAllColumnsMenuItem_actionPerformed(e);
- }
- });
- remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
+ remove2LeftMenuItem.setText("Remove Left");
remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
remove2LeftMenuItem_actionPerformed(e);
}
});
- remove2RightMenuItem.setText("Remove sequence -> right of selected column");
+ remove2RightMenuItem.setText("Remove Right");
remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
remove2RightMenuItem_actionPerformed(e);
}
});
- removeGappedColumnMenuItem.setText("Remove gapped columns");
- removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
+ removeGappedColumnMenuItem.setText("Remove Empty Columns");
+ removeGappedColumnMenuItem.addActionListener(new java.awt.event.
+ ActionListener()
{
public void actionPerformed(ActionEvent e)
{
removeGappedColumnMenuItem_actionPerformed(e);
}
});
- removeAllGapsMenuItem.setText("Remove all gaps");
+ removeAllGapsMenuItem.setText("Remove All Gaps");
removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
removeAllGapsMenuItem_actionPerformed(e);
}
});
- setGapCharMenuItem.setText("Set gap character to \".\"");
- setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- setGapCharMenuItem_actionPerformed(e);
- }
- });
viewBoxesMenuItem.setText("Boxes");
viewBoxesMenuItem.setState(true);
viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
viewTextMenuItem_actionPerformed(e);
}
});
- sortPairwiseMenuItem.setText("Sort by pairwise identity");
+ sortPairwiseMenuItem.setText("by Pairwise Identity");
sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
sortPairwiseMenuItem_actionPerformed(e);
}
});
- sortIDMenuItem.setText("Sort by ID");
+ sortIDMenuItem.setText("by ID");
sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
sortIDMenuItem_actionPerformed(e);
}
});
- sortGroupMenuItem.setText("Sort by group");
+ sortGroupMenuItem.setText("by Group");
sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
sortGroupMenuItem_actionPerformed(e);
}
});
- sortTreeOrderMenuItem.setText("Sort by tree order");
- sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- sortTreeOrderMenuItem_actionPerformed(e);
- }
- });
- removeRedundancyMenuItem.setText("Remove redundancy");
- removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
+ removeRedundancyMenuItem.setText("Remove Redundancy...");
+ removeRedundancyMenuItem.addActionListener(new java.awt.event.
+ ActionListener()
{
public void actionPerformed(ActionEvent e)
{
removeRedundancyMenuItem_actionPerformed(e);
}
});
- pairwiseAlignmentMenuItem.setText("Pairwise alignments");
- pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
+ pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
+ pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
+ ActionListener()
{
public void actionPerformed(ActionEvent e)
{
pairwiseAlignmentMenuItem_actionPerformed(e);
}
});
- PCAMenuItem.setText("Principal component analysis");
+ PCAMenuItem.setText("Principal Component Analysis");
PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
PCAMenuItem_actionPerformed(e);
}
});
- averageDistanceTreeMenuItem.setText("Average distance tree using PID");
- averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+ averageDistanceTreeMenuItem.setText(
+ "Average Distance Using % Identity");
+ averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
+ ActionListener()
{
public void actionPerformed(ActionEvent e)
{
averageDistanceTreeMenuItem_actionPerformed(e);
}
});
- neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
+ neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
neighbourTreeMenuItem_actionPerformed(e);
}
});
- clustalAlignMenuItem.setText("Clustal alignment");
- clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- clustalAlignMenuItem_actionPerformed(e);
- }
- });
this.getContentPane().setLayout(borderLayout1);
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBackground(Color.white);
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
statusBar.setText("Status bar");
outputTextboxMenu.setMnemonic('T');
- outputTextboxMenu.setText("Output alignment via textbox");
- clustalColour.setSelected(false);
- clustalColour.setText("Clustalx colours");
+ outputTextboxMenu.setText("Output to Textbox");
+ clustalColour.setText("Clustalx");
+
clustalColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
clustalColour_actionPerformed(e);
}
});
- zappoColour.setText("Zappo colour scheme");
+ zappoColour.setText("Zappo");
zappoColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
zappoColour_actionPerformed(e);
}
});
- taylorColour.setText("Taylor colour scheme");
+ taylorColour.setText("Taylor");
taylorColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
taylorColour_actionPerformed(e);
}
});
- hydrophobicityColour.setText("By hydrophobicity");
+ hydrophobicityColour.setText("Hydrophobicity");
hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
hydrophobicityColour_actionPerformed(e);
}
});
- helixColour.setText("Helix propensity");
+ helixColour.setText("Helix Propensity");
helixColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
helixColour_actionPerformed(e);
}
});
- strandColour.setText("Strand propensity");
+ strandColour.setText("Strand Propensity");
strandColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
strandColour_actionPerformed(e);
}
});
- turnColour.setText("Turn propensity");
+ turnColour.setText("Turn Propensity");
turnColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
turnColour_actionPerformed(e);
}
});
- buriedColour.setText("Buried index");
+ buriedColour.setText("Buried Index");
buriedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
buriedColour_actionPerformed(e);
}
});
- userDefinedColour.setText("User defined colours");
+ userDefinedColour.setText("User Defined...");
userDefinedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
PIDColour_actionPerformed(e);
}
});
- BLOSUM62Colour.setText("BLOSUM62 score");
+ BLOSUM62Colour.setText("BLOSUM62 Score");
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
BLOSUM62Colour_actionPerformed(e);
}
});
- avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
- avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+ avDistanceTreeBlosumMenuItem.setText(
+ "Average Distance Using BLOSUM62");
+ avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
+ ActionListener()
{
public void actionPerformed(ActionEvent e)
{
avTreeBlosumMenuItem_actionPerformed(e);
}
});
- njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
+ njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
annotationPanelMenuItem.setActionCommand("");
- annotationPanelMenuItem.setText("Annotation Panel");
- annotationPanelMenuItem.setState(true);
+ annotationPanelMenuItem.setText("Show Annotations");
+ annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
annotationPanelMenuItem_actionPerformed(e);
}
});
- colourTextMenuItem.setText("Colour text");
+ colourTextMenuItem.setText("Colour Text");
colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
colourTextMenuItem_actionPerformed(e);
}
});
- htmlMenuItem.setText("Output as HTML");
+ htmlMenuItem.setText("HTML");
htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
htmlMenuItem_actionPerformed(e);
}
});
- overviewMenuItem.setText("Overview window");
+ overviewMenuItem.setText("Overview Window");
overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
undoMenuItem.setEnabled(false);
undoMenuItem.setMnemonic('Z');
undoMenuItem.setText("Undo");
+ undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_Z,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
undoMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
redoMenuItem_actionPerformed(e);
}
});
- conservationMenuItem.setText("By conservation");
+ conservationMenuItem.setText("By Conservation");
conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
noColourmenuItem.setText("None");
- noColourmenuItem.setSelected(true);
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
noColourmenuItem_actionPerformed(e);
}
});
- wrapMenuItem.setText("Wrap alignment");
+ wrapMenuItem.setText("Wrap");
wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
printMenuItem_actionPerformed(e);
}
});
- renderGapsMenuItem.setText("Render gaps");
+ renderGapsMenuItem.setText("Show Gaps");
renderGapsMenuItem.setState(true);
renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
{
renderGapsMenuItem_actionPerformed(e);
}
});
- findMenuItem.setText("Find");
+ findMenuItem.setText("Find...");
+ findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_F,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
findMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
});
searchMenu.setText("Search");
- abovePIDThreshold.setText("Above PID threshold");
- abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent e) {
+ abovePIDThreshold.setText("Above Identity Threshold");
+ abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
abovePIDThreshold_actionPerformed(e);
}
});
- sequenceFeatures.setText("Sequence Features");
- sequenceFeatures.addActionListener(new ActionListener()
+ showSeqFeatures.setText("Show Sequence Features");
+ showSeqFeatures.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent actionEvent)
{
- sequenceFeatures_actionPerformed(actionEvent);
+ showSeqFeatures_actionPerformed(actionEvent);
}
});
- nucleotideColour.setText("Nucleotide colours");
+ nucleotideColour.setText("Nucleotide");
nucleotideColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
nucleotideColour_actionPerformed(e);
}
});
- deleteGroups.setSelected(false);
- deleteGroups.setText("Delete all groups");
+ deleteGroups.setText("Undefine groups");
deleteGroups.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
}
});
copy.setText("Copy");
+ copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_C,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
copy.setMnemonic(KeyEvent.VK_C);
copy.addActionListener(new java.awt.event.ActionListener()
}
});
cut.setText("Cut");
+ cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_X,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
cut.setMnemonic(KeyEvent.VK_X);
cut.addActionListener(new java.awt.event.ActionListener()
{
});
jMenu1.setMnemonic('V');
jMenu1.setText("Paste");
- pasteNew.setText("to new alignment");
+ pasteNew.setText("To New Alignment");
+ pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+ java.awt.event.KeyEvent.VK_V,
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
pasteNew.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
pasteNew_actionPerformed(e);
}
});
- pasteThis.setText("add to this alignment");
+ pasteThis.setText("Add To This Alignment");
pasteThis.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
pasteThis_actionPerformed(e);
}
});
- applyToAllGroups.setText("Apply colour to all groups");
+ applyToAllGroups.setText("Apply Colour To All Groups");
applyToAllGroups.setState(true);
applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
{
{
public void actionPerformed(ActionEvent e)
{
- createPNG_actionPerformed(e);
+ createPNG(null);
}
});
- createPNG.setActionCommand("Save as PNG Image");
- createPNG.setText("Save as PNG Image");
- font.setText("Change Font");
+ createPNG.setActionCommand("Save As PNG Image");
+ createPNG.setText("PNG");
+ font.setText("Font...");
font.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
font_actionPerformed(e);
}
});
- fullSeqId.setText("Show full sequence id");
- fullSeqId.addActionListener(new java.awt.event.ActionListener()
+
+ seqLimits.setText("Show Sequence Limits");
+ seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
+ seqLimits.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- fullSeqId_actionPerformed(e);
+ seqLimit_actionPerformed(e);
}
});
- epsFile.setText("Save as EPS file");
+ epsFile.setText("EPS");
epsFile.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- epsFile_actionPerformed(e);
+ createEPS(null);
}
});
LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
- LoadtreeMenuItem.setText("Load assocated tree");
- LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
+ LoadtreeMenuItem.setText("Load Associated Tree");
+ LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
public void actionPerformed(ActionEvent e)
{
LoadtreeMenuItem_actionPerformed(e);
}
});
- jpred.setText("JPred");
- jpred.addActionListener(new java.awt.event.ActionListener()
+ scaleAbove.setVisible(false);
+ scaleAbove.setText("Scale Above");
+ scaleAbove.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ scaleAbove_actionPerformed(e);
+ }
+ });
+ scaleLeft.setVisible(false);
+ scaleLeft.setSelected(true);
+ scaleLeft.setText("Scale Left");
+ scaleLeft.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ scaleLeft_actionPerformed(e);
+ }
+ });
+ scaleRight.setVisible(false);
+ scaleRight.setSelected(true);
+ scaleRight.setText("Scale Right");
+ scaleRight.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ scaleRight_actionPerformed(e);
+ }
+ });
+ modifyPID.setText("Modify Identity Threshold...");
+ modifyPID.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyPID_actionPerformed(e);
+ }
+ });
+ modifyConservation.setText("Modify Conservation Threshold...");
+ modifyConservation.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed(e);
+ }
+ });
+ sortByTreeMenu.setText("By Tree Order");
+ sort.setText("Sort");
+ calculate.setText("Calculate Tree");
+
+ jMenu2.setText("Export");
+ padGapsMenuitem.setText("Pad Gaps");
+ padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
+ padGapsMenuitem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ padGapsMenuitem_actionPerformed(e);
+ }
+ });
+ vamsasStore.setVisible(false);
+ vamsasStore.setText("VAMSAS store");
+ vamsasStore.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ vamsasStore_actionPerformed(e);
+ }
+ });
+ showTranslation.setText("Translate cDNA");
+ showTranslation.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showTranslation_actionPerformed(e);
+ }
+ });
+
+ /* tabbedPane.addChangeListener(new ChangeListener()
+ {
+ public void stateChanged(ChangeEvent ece)
+ {
+
+ tabSelected();
+ }
+ });*/
+ featureSettings.setText("Feature Settings...");
+ featureSettings.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ featureSettings_actionPerformed(e);
+ }
+ });
+ fetchSequence.setText("Fetch Sequence(s)...");
+ fetchSequence.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ fetchSequence_actionPerformed(e);
+ }
+ });
+ smoothFont.setText("Smooth Fonts");
+ smoothFont.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ smoothFont_actionPerformed(e);
+ }
+ });
+ smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));
+ annotationColour.setText("By Annotation...");
+ annotationColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationColour_actionPerformed(e);
+ }
+ });
+ associatedData.setText("Load Features / Annotations");
+ associatedData.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ associatedData_actionPerformed(e);
+ }
+ });
+ autoCalculate.setText("Autocalculate Consensus");
+ autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+ autoCalculate.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ autoCalculate_actionPerformed(e);
+ }
+ });
+ addSequenceMenu.setText("Add Sequences");
+ addFromFile.setText("From File");
+ addFromFile.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ addFromFile_actionPerformed(e);
+ }
+ });
+ addFromText.setText("From Textbox");
+ addFromText.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ addFromText_actionPerformed(e);
+ }
+ });
+ addFromURL.setText("From URL");
+ addFromURL.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ addFromURL_actionPerformed(e);
+ }
+ });
+ exportFeatures.setText("Export Features...");
+ exportFeatures.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ exportFeatures_actionPerformed(e);
+ }
+ });
+ exportAnnotations.setText("Export Annotations...");
+ exportAnnotations.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ exportAnnotations_actionPerformed(e);
+ }
+ });
+ statusPanel.setLayout(gridLayout1);
+ jMenu3.setText("Show");
+ showAllSeqs.setText("All Sequences");
+ showAllSeqs.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllSeqs_actionPerformed(e);
+ }
+ });
+ showAllColumns.setText("All Columns");
+ showAllColumns.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllColumns_actionPerformed(e);
+ }
+ });
+ jMenu4.setText("Hide");
+ hideSelSequences.setText("Selected Sequences");
+ hideSelSequences.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSelSequences_actionPerformed(e);
+ }
+ });
+ hideSelColumns.setText("Selected Columns");
+ hideSelColumns.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSelColumns_actionPerformed(e);
+ }
+ });
+ hiddenMarkers.setText("Hidden Markers");
+ hiddenMarkers.setState(true);
+ hiddenMarkers.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hiddenMarkers_actionPerformed(e);
+ }
+ });
+ invertColSel.setText("Invert Column Selection");
+ invertColSel.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- jpred_actionPerformed(e);
+ invertColSel_actionPerformed(e);
}
});
+
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
alignFrameMenuBar.add(searchMenu);
alignFrameMenuBar.add(viewMenu);
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
- alignFrameMenuBar.add(alignMenu);
+ alignFrameMenuBar.add(webService);
+ fileMenu.add(addSequenceMenu);
+ fileMenu.add(fetchSequence);
+ fileMenu.addSeparator();
+ fileMenu.add(vamsasStore);
fileMenu.add(saveAlignmentMenu);
+ fileMenu.add(jMenu2);
fileMenu.add(outputTextboxMenu);
- fileMenu.add(htmlMenuItem);
- fileMenu.add(epsFile);
- fileMenu.add(createPNG);
fileMenu.add(printMenuItem);
fileMenu.addSeparator();
+ fileMenu.add(exportFeatures);
+ fileMenu.add(exportAnnotations);
fileMenu.add(LoadtreeMenuItem);
+ fileMenu.add(associatedData);
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
+ editMenu.add(undoMenuItem);
+ editMenu.add(redoMenuItem);
+ editMenu.add(cut);
editMenu.add(copy);
editMenu.add(jMenu1);
- editMenu.add(cut);
editMenu.add(delete);
editMenu.addSeparator();
- editMenu.add(undoMenuItem);
- editMenu.add(redoMenuItem);
- editMenu.addSeparator();
- editMenu.add(deselectAllSequenceMenuItem);
editMenu.add(selectAllSequenceMenuItem);
+ editMenu.add(deselectAllSequenceMenuItem);
editMenu.add(invertSequenceMenuItem);
+ editMenu.add(invertColSel);
editMenu.add(deleteGroups);
- editMenu.add(groupsMenuItem);
editMenu.addSeparator();
- editMenu.add(deselectAllColumnsMenuItem);
editMenu.add(remove2LeftMenuItem);
editMenu.add(remove2RightMenuItem);
- editMenu.addSeparator();
editMenu.add(removeGappedColumnMenuItem);
editMenu.add(removeAllGapsMenuItem);
- editMenu.add(setGapCharMenuItem);
+ editMenu.add(removeRedundancyMenuItem);
+ editMenu.addSeparator();
+ editMenu.add(padGapsMenuitem);
searchMenu.add(findMenuItem);
viewMenu.add(font);
- viewMenu.add(fullSeqId);
+ viewMenu.add(smoothFont);
+ viewMenu.addSeparator();
+ viewMenu.add(jMenu3);
+ viewMenu.add(jMenu4);
+ viewMenu.add(hiddenMarkers);
+ viewMenu.addSeparator();
viewMenu.add(wrapMenuItem);
+ viewMenu.add(seqLimits);
+ viewMenu.add(scaleAbove);
+ viewMenu.add(scaleLeft);
+ viewMenu.add(scaleRight);
viewMenu.add(viewBoxesMenuItem);
viewMenu.add(viewTextMenuItem);
viewMenu.add(colourTextMenuItem);
viewMenu.add(renderGapsMenuItem);
viewMenu.add(annotationPanelMenuItem);
+ viewMenu.addSeparator();
+ viewMenu.add(showSeqFeatures);
+ viewMenu.add(featureSettings);
+ viewMenu.addSeparator();
viewMenu.add(overviewMenuItem);
- viewMenu.add(sequenceFeatures);
colourMenu.add(applyToAllGroups);
+ colourMenu.addSeparator();
colourMenu.add(noColourmenuItem);
colourMenu.add(clustalColour);
+ colourMenu.add(BLOSUM62Colour);
+ colourMenu.add(PIDColour);
colourMenu.add(zappoColour);
colourMenu.add(taylorColour);
colourMenu.add(hydrophobicityColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
colourMenu.add(userDefinedColour);
- colourMenu.add(PIDColour);
- colourMenu.add(BLOSUM62Colour);
colourMenu.addSeparator();
- colourMenu.add(abovePIDThreshold);
colourMenu.add(conservationMenuItem);
- calculateMenu.add(sortPairwiseMenuItem);
- calculateMenu.add(sortIDMenuItem);
- calculateMenu.add(sortGroupMenuItem);
- calculateMenu.add(sortTreeOrderMenuItem);
- calculateMenu.add(removeRedundancyMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDThreshold);
+ colourMenu.add(modifyPID);
+ colourMenu.add(annotationColour);
+ calculateMenu.add(sort);
+ calculateMenu.add(calculate);
calculateMenu.addSeparator();
calculateMenu.add(pairwiseAlignmentMenuItem);
calculateMenu.add(PCAMenuItem);
calculateMenu.addSeparator();
- calculateMenu.add(averageDistanceTreeMenuItem);
- calculateMenu.add(neighbourTreeMenuItem);
- calculateMenu.add(avDistanceTreeBlosumMenuItem);
- calculateMenu.add(njTreeBlosumMenuItem);
- alignMenu.add(clustalAlignMenuItem);
- alignMenu.add(jpred);
- this.getContentPane().add(statusBar, BorderLayout.SOUTH);
- jMenu1.add(pasteNew);
+ calculateMenu.add(showTranslation);
+ calculateMenu.add(autoCalculate);
+ webServiceNoServices=new JMenuItem("<No Services>");
+ webService.add(webServiceNoServices);jMenu1.add(pasteNew);
jMenu1.add(pasteThis);
+ sort.add(sortIDMenuItem);
+ sort.add(sortGroupMenuItem);
+ sort.add(sortPairwiseMenuItem);
+ calculate.add(averageDistanceTreeMenuItem);
+ calculate.add(neighbourTreeMenuItem);
+ calculate.add(avDistanceTreeBlosumMenuItem);
+ calculate.add(njTreeBlosumMenuItem);
+ jMenu2.add(htmlMenuItem);
+ jMenu2.add(epsFile);
+ jMenu2.add(createPNG);
+ addSequenceMenu.add(addFromFile);
+ addSequenceMenu.add(addFromText);
+ addSequenceMenu.add(addFromURL);
+ this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
+ statusPanel.add(statusBar, null);
+ jMenu3.add(showAllColumns);
+ jMenu3.add(showAllSeqs);
+ jMenu4.add(hideSelColumns);
+ jMenu4.add(hideSelSequences);
}
- protected void saveAs_actionPerformed(ActionEvent e)
+ protected void outputText_actionPerformed(ActionEvent e)
{
-
}
- protected void outputText_actionPerformed(ActionEvent e)
+ public void addFromFile_actionPerformed(ActionEvent e)
{
}
- protected void htmlMenuItem_actionPerformed(ActionEvent e)
+ public void addFromText_actionPerformed(ActionEvent e)
{
}
-
-
-
-
- protected void closeMenuItem_actionPerformed(ActionEvent e)
+ public void addFromURL_actionPerformed(ActionEvent e)
{
}
- protected void redoMenuItem_actionPerformed(ActionEvent e)
+ public void exportFeatures_actionPerformed(ActionEvent e)
{
}
- protected void undoMenuItem_actionPerformed(ActionEvent e)
+ public void exportAnnotations_actionPerformed(ActionEvent e)
{
}
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
- protected void groupsMenuItem_actionPerformed(ActionEvent e)
+ protected void closeMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void redoMenuItem_actionPerformed(ActionEvent e)
+ {
}
+ protected void undoMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
{
-
- }
-
-
- protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
- {
-
}
protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
-
}
- protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
- {
-
- }
-
-
-
-
-
protected void wrapMenuItem_actionPerformed(ActionEvent e)
{
-
}
-
protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void viewTextMenuItem_actionPerformed(ActionEvent e)
{
-
}
-
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
-
}
-
-
protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void overviewMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void sortIDMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
-
- }
-
- protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
- {
-
}
protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void PCAMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
-
}
-
protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
-
}
protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void clustalColour_actionPerformed(ActionEvent e)
+ {
}
+ protected void zappoColour_actionPerformed(ActionEvent e)
+ {
+ }
+ protected void taylorColour_actionPerformed(ActionEvent e)
+ {
+ }
- protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
+ protected void hydrophobicityColour_actionPerformed(ActionEvent e)
{
+ }
+ protected void helixColour_actionPerformed(ActionEvent e)
+ {
}
+ protected void strandColour_actionPerformed(ActionEvent e)
+ {
+ }
+ protected void turnColour_actionPerformed(ActionEvent e)
+ {
+ }
+ protected void buriedColour_actionPerformed(ActionEvent e)
+ {
+ }
- protected void clustalColour_actionPerformed(ActionEvent e)
+ protected void userDefinedColour_actionPerformed(ActionEvent e)
{
+ }
+ protected void PIDColour_actionPerformed(ActionEvent e)
+ {
}
- protected void zappoColour_actionPerformed(ActionEvent e)
+ protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
{
+ }
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ {
}
- protected void taylorColour_actionPerformed(ActionEvent e)
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void printMenuItem_actionPerformed(ActionEvent e)
+ {
}
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+ protected void findMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void abovePIDThreshold_actionPerformed(ActionEvent e)
+ {
}
- protected void helixColour_actionPerformed(ActionEvent e)
+ public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
{
+ }
+ protected void nucleotideColour_actionPerformed(ActionEvent e)
+ {
}
- protected void strandColour_actionPerformed(ActionEvent e)
+ protected void deleteGroups_actionPerformed(ActionEvent e)
{
+ }
+ protected void copy_actionPerformed(ActionEvent e)
+ {
}
- protected void turnColour_actionPerformed(ActionEvent e)
+ protected void cut_actionPerformed(ActionEvent e)
{
+ }
+ protected void delete_actionPerformed(ActionEvent e)
+ {
}
- protected void buriedColour_actionPerformed(ActionEvent e)
+ protected void pasteNew_actionPerformed(ActionEvent e)
{
+ }
+ protected void pasteThis_actionPerformed(ActionEvent e)
+ {
}
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ {
+ }
+ public void createPNG(java.io.File f)
+ {
+ }
- protected void userDefinedColour_actionPerformed(ActionEvent e)
+ protected void font_actionPerformed(ActionEvent e)
{
+ }
+ protected void seqLimit_actionPerformed(ActionEvent e)
+ {
}
- protected void PIDColour_actionPerformed(ActionEvent e)
+ public void seqDBRef_actionPerformed(ActionEvent e)
{
}
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+
+ public void createEPS(java.io.File f)
{
+ }
+ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+ {
}
+ protected void jpred_actionPerformed(ActionEvent e)
+ {
+ }
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ protected void scaleAbove_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void scaleLeft_actionPerformed(ActionEvent e)
{
+ }
+ protected void scaleRight_actionPerformed(ActionEvent e)
+ {
}
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ protected void modifyPID_actionPerformed(ActionEvent e)
{
+ }
+ protected void modifyConservation_actionPerformed(ActionEvent e)
+ {
}
- protected void printMenuItem_actionPerformed(ActionEvent e)
+
+ protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
{
+ }
+ protected void padGapsMenuitem_actionPerformed(ActionEvent e)
+ {
}
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+
+ public void vamsasStore_actionPerformed(ActionEvent e)
{
}
- protected void findMenuItem_actionPerformed(ActionEvent e)
+ public void vamsasLoad_actionPerformed(ActionEvent e)
{
}
-
- protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
+ public void showTranslation_actionPerformed(ActionEvent e)
+ {
}
- public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
+ public void featureSettings_actionPerformed(ActionEvent e)
{
}
- protected void nucleotideColour_actionPerformed(ActionEvent e)
+ public void fetchSequence_actionPerformed(ActionEvent e)
{
}
- protected void deleteGroups_actionPerformed(ActionEvent e)
+ public void smoothFont_actionPerformed(ActionEvent e)
{
}
- protected void copy_actionPerformed(ActionEvent e)
+ public void annotationColour_actionPerformed(ActionEvent e)
{
}
- protected void cut_actionPerformed(ActionEvent e)
+ public void associatedData_actionPerformed(ActionEvent e)
{
}
- protected void delete_actionPerformed(ActionEvent e)
+ public void autoCalculate_actionPerformed(ActionEvent e)
{
}
- protected void pasteNew_actionPerformed(ActionEvent e)
+ public void showAllSeqs_actionPerformed(ActionEvent e)
{
}
- protected void pasteThis_actionPerformed(ActionEvent e)
+ public void showAllColumns_actionPerformed(ActionEvent e)
{
}
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ public void hideSelSequences_actionPerformed(ActionEvent e)
{
}
- protected void createPNG_actionPerformed(ActionEvent e)
+ public void hideSelColumns_actionPerformed(ActionEvent e)
{
}
- protected void font_actionPerformed(ActionEvent e)
+ public void hiddenMarkers_actionPerformed(ActionEvent e)
{
}
- protected void fullSeqId_actionPerformed(ActionEvent e)
+ public void findPdbId_actionPerformed(ActionEvent e)
{
}
- protected void epsFile_actionPerformed(ActionEvent e)
+ public void enterPdbId_actionPerformed(ActionEvent e)
{
}
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+ public void pdbFile_actionPerformed(ActionEvent e)
+ {
}
- protected void jpred_actionPerformed(ActionEvent e)
+ public void invertColSel_actionPerformed(ActionEvent e)
{
}
-
}
git://source.jalview.org / jalview.git / blobdiff